docs

R/display.R

@@ -2,7 +2,9 @@
 #' @name display.parameters_model
 #'
 #' @description Prints tables (i.e. data frame) in different output formats.
-#'   `print_md()` is a alias for `display(format = "markdown")`.
+#' `print_md()` is a alias for `display(format = "markdown")`, `print_html()`
+#' is a alias for `display(format = "html")`. `print_table()` is for specific
+#' use cases only, and currently only works for `compare_parameters()` objects.
 #'
 #' @param x An object returned by [`model_parameters()`][model_parameters].
 #' @param object An object returned by [`model_parameters()`][model_parameters],

R/methods_glmmTMB.R

@@ -320,22 +320,20 @@ standard_error.glmmTMB <- function(model,
   )
 
   if (effects == "random") {
-    if (requireNamespace("TMB", quietly = TRUE) && requireNamespace("glmmTMB", quietly = TRUE)) {
-      s1 <- TMB::sdreport(model$obj, getJointPrecision = TRUE)
-      s2 <- sqrt(s1$diag.cov.random)
-      rand.ef <- glmmTMB::ranef(model)[[1]]
-      rand.se <- lapply(rand.ef, function(.x) {
-        cnt <- nrow(.x) * ncol(.x)
-        s3 <- s2[1:cnt]
-        s2 <- s2[-(1:cnt)]
-        d <- as.data.frame(matrix(sqrt(s3), ncol = ncol(.x), byrow = TRUE))
-        colnames(d) <- colnames(.x)
-        d
-      })
-      rand.se
-    } else {
+    if (!requireNamespace("TMB", quietly = TRUE) && !requireNamespace("glmmTMB", quietly = TRUE)) {
       return(NULL)
     }
+    s1 <- TMB::sdreport(model$obj, getJointPrecision = TRUE)
+    s2 <- sqrt(s1$diag.cov.random)
+    rand.ef <- glmmTMB::ranef(model)[[1]]
+    rand.se <- lapply(rand.ef, function(.x) {
+      cnt <- nrow(.x) * ncol(.x)
+      s3 <- s2[1:cnt]
+      s2 <- s2[-(1:cnt)]
+      d <- as.data.frame(matrix(sqrt(s3), ncol = ncol(.x), byrow = TRUE))
+      colnames(d) <- colnames(.x)
+      d
+    })
   } else {
     if (is.null(.check_component(model, component, verbose = verbose))) {
       return(NULL)

R/methods_lme4.R

@@ -82,29 +82,24 @@
 #' use `effects = "fixed"`. There is also a [`plot()`-method](https://easystats.github.io/see/articles/parameters.html)
 #' implemented in the [**see**-package](https://easystats.github.io/see/).
 #'
-#' @examples
+#' @examplesIf require("lme4") && require("glmmTMB")
 #' library(parameters)
-#' if (require("lme4")) {
-#'   data(mtcars)
-#'   model <- lmer(mpg ~ wt + (1 | gear), data = mtcars)
-#'   model_parameters(model)
-#' }
+#' data(mtcars)
+#' model <- lme4::lmer(mpg ~ wt + (1 | gear), data = mtcars)
+#' model_parameters(model)
+#'
 #' \donttest{
-#' if (require("glmmTMB")) {
-#'   data(Salamanders)
-#'   model <- glmmTMB(
-#'     count ~ spp + mined + (1 | site),
-#'     ziformula = ~mined,
-#'     family = poisson(),
-#'     data = Salamanders
-#'   )
-#'   model_parameters(model, effects = "all")
-#' }
+#' data(Salamanders, package = "glmmTMB")
+#' model <- glmmTMB::glmmTMB(
+#'   count ~ spp + mined + (1 | site),
+#'   ziformula = ~mined,
+#'   family = poisson(),
+#'   data = Salamanders
+#' )
+#' model_parameters(model, effects = "all")
 #'
-#' if (require("lme4")) {
-#'   model <- lmer(mpg ~ wt + (1 | gear), data = mtcars)
-#'   model_parameters(model, bootstrap = TRUE, iterations = 50, verbose = FALSE)
-#' }
+#' model <- lme4::lmer(mpg ~ wt + (1 | gear), data = mtcars)
+#' model_parameters(model, bootstrap = TRUE, iterations = 50, verbose = FALSE)
 #' }
 #' @return A data frame of indices related to the model's parameters.
 #' @export

R/print_html.R

@@ -233,7 +233,7 @@ print_html.compare_parameters <- function(x,
   if (!is.null(user_labels)) {
     new_labels <- c(
       colnames(out[["_data"]])[1],
-      rep(user_labels, length.out = ncol(out[["_data"]]) - 1)
+      rep_len(user_labels, ncol(out[["_data"]]) - 1)
     )
     new_labels <- as.list(new_labels)
   }
@@ -270,7 +270,7 @@ print_html.compare_parameters <- function(x,
   # check where last parameter row ends. For "compare_models()", the
   # first Parameter value after data rows is "". If this is not found,
   # simply use number of rows as last row
-  last_row <- which(out[["_data"]][[pcol_name]] == "")[1]
+  last_row <- which(!nzchar(as.character(out[["_data"]][[pcol_name]]), keepNA = TRUE))[1]
   if (is.na(last_row)) {
     last_row <- nrow(out[["_data"]])
   } else {

R/print_table.R

@@ -1,3 +1,22 @@
+#' @examplesIf require("tinytable") && require("lme4") && require("glmmTMB")
+#' \donttest{
+#' data(iris)
+#' data(Salamanders, package = "glmmTMB")
+#' m1 <- lm(Sepal.Length ~ Species * Petal.Length, data = iris)
+#' m2 <- lme4::lmer(
+#'   Sepal.Length ~ Petal.Length + Petal.Width + (1 | Species),
+#'   data = iris
+#' )
+#' m3 <- glmmTMB::glmmTMB(
+#'   count ~ spp + mined + (1 | site),
+#'   ziformula = ~mined,
+#'   family = poisson(),
+#'   data = Salamanders
+#' )
+#' out <- compare_parameters(m1, m2, m3, effects = "all", components = "all")
+#' print_table(out)
+#'
+#' @rdname display.parameters_model
 #' @export
 print_table <- function(x, digits = 2, p_digits = 3, ...) {
   insight::check_if_installed(c("datawizard", "tinytable"))